The complexes [Mo₁₂O₁₂S₁₂(OH)₁₂(Muco)]²⁻ (Muco²⁻ = muconate, C₆H₄O₄²⁻) and [Mo₁₂O₁₂S₁₂(OH)₁₂(TMT)]²⁻ (TMT²⁻ = tetramethylterephthalate, C₁₂H₁₂O₄²⁻) have been obtained from the condensation of the [Mo₂O₂S₂]²⁺ building block in the presence of Muco²⁻ and TMT²⁻, respectively. Both compounds were structurally characterized, revealing host–guest architectures with one or two encapsulated water molecules. ¹H NMR spectra in DMSO and D₂O showed that both complexes had an average symmetry higher than that in the solid state, due to changes in the distribution of encapsulated water molecules. The relative stabilities in water of the seven complexes encapsulating various di- or tricarboxylate guests, either rigid or non-rigid, have been determined. The stability scale obtained for the dianionic complexes is interpreted in relation with the rigidity or flexibility of the guests. A DFT study demonstrates that additional stabilization arises from the presence of inner hydrogen bonds involving 1, 2 or 3 water molecules, which even permit the extension of the H-bonds network to the first solvation sphere of the anion. DFT calculations were carried out on all investigated complexes as isolated or solvated anions and provide the sequence of the bond energies between the host and the guests, which is compared to the experimental data.